Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Science Advances, Journal Year: 2023, Volume and Issue: 9(7)

Published: Feb. 17, 2023

Early natural historians—Comte de Buffon, von Humboldt, and De Candolle—established environment geography as two principal axes determining the distribution of groups organisms, laying foundations for biogeography over subsequent 200 years, yet relative importance these remains unresolved. Leveraging phylogenomic global species data Mimosoid legumes, a pantropical plant clade c. 3500 species, we show that water availability gradient from deserts to rain forests dictates turnover lineages within continents across tropics. We demonstrate 95% speciation occurs precipitation niche, showing profound phylogenetic niche conservatism, lineage boundaries coincide with isohyets precipitation. reveal similar patterns on different continents, implying evolution dispersal follow universal processes.

Language: Английский

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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification

PhytoKeys, Journal Year: 2024, Volume and Issue: 240, P. 1 - 552

Published: April 3, 2024

Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It an ecologically economically important group formed mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas shrubs, which has a global distribution, occurring on every continent except Antarctica. Following recent re-circumscription 15 genera as presented in Advances Legume Systematics 14, Part 1, using basis phylogenomic analysis 997 nuclear gene sequences for 420 all but five currently recognised subfamily, we present new higher-level classification subfamily. The comprises eleven tribes, are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 / 223 species), Campsiandreae LPWG (2 5–22), Cassieae Bronn (7 695), Ceratonieae (4 6), Dimorphandreae Benth. 35), Erythrophleeae /13), Gleditsieae Nakai (3 20), Mimoseae (100 3510), Pterogyneae (1 1), Schizolobieae (8 42–43), Sclerolobieae & Hook. f. (5 113). Although many these lineages have been named past, tribes informal generic groups, their circumscriptions varied widely changed over past decades, such described here differ membership those previously recognised. Importantly, approximately 3500 100 former Mimosoideae now placed reinstated, newly circumscribed, tribe Mimoseae. Because size ecological importance tribe, also provide clade-based system includes 17 lower-level clades. Fourteen remain unplaced clades: eight resolved two grades six phylogenetically isolated monogeneric lineages. In addition classification, key genera, morphological descriptions notes diversity growth forms, foliage, flowers fruits illustrated each genus distribution map, based quality-controlled herbarium specimen localities. A glossary specialised terms used legume morphology provided. This provides solid communication framework downstream analyses biogeography, trait evolution diversification, well taxonomic revision still understudied

Language: Английский

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Genomes, fossils, and the concurrent rise of modern birds and flowering plants in the Late Cretaceous

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(8)

Published: Feb. 12, 2024

The phylogeny and divergence timing of the Neoavian radiation remain controversial despite recent progress. We analyzed genomes 124 species across all orders, using data from 25,460 loci spanning four DNA classes, including 5,756 coding sequences, 12,449 conserved nonexonic elements, 4,871 introns, 2,384 intergenic segments. conducted a comprehensive sensitivity analysis to account for heterogeneity different leading an optimal tree Neoaves with high resolution. This features novel dichotomy comprising two monophyletic clades: previously recognized Telluraves (land birds) newly circumscribed Aquaterraves (waterbirds relatives). Molecular dating analyses 20 fossil calibrations indicate that diversification modern birds began in Late Cretaceous underwent constant steady KPg boundary, concurrent rise angiosperms as well other major Cenozoic animal groups placental multituberculate mammals. catastrophe had limited impact on avian evolution compared Paleocene–Eocene Thermal Maximum, which triggered rapid seabirds. Our findings suggest followed slow process gradualism rather than punctuated equilibrium, interruption by catastrophe. study places bird into new context within vertebrates, ramifications Earth’s biota.

Language: Английский

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Common Methods for Phylogenetic Tree Construction and Their Implementation in R

Bioengineering, Journal Year: 2024, Volume and Issue: 11(5), P. 480 - 480

Published: May 11, 2024

A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing trees, including distance methods, maximum parsimony, likelihood, Bayesian inference, tree-integration (supermatrix supertree). Here discuss advantages, shortcomings, applications of each method offer relevant codes to construct trees from molecular data using packages algorithms R. This review aims provide comprehensive guidance reference researchers seeking while also promoting further development innovation field. By offering clear concise overview different available, hope enable select most appropriate approach their specific research questions datasets.

Language: Английский

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Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 21, 2025

Abstract Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting (ILS), duplication loss (GDL), horizontal transfer (HGT) can complicate the estimation of species lengths. While several tools exist topology a addressing various causes discordance, much less attention has been paid length on multi-locus datasets. For single-copy trees, some methods available that summarize onto tree, including coalescent-based account ILS. no method exists multi-copy family trees have evolved with loss. To address this gap, we introduce CASTLES-Pro algorithm while accounting both GDL improves existing CASTLES by increasing its accuracy extends it handle ones. Our simulation studies show is generally more accurate than alternatives, eliminating systematic bias toward overestimating terminal often observed when using concatenation. Moreover, not theoretically designed HGT, maintains relatively high under rates random HGT. Code availability implemented inside software package ASTER, at https://github.com/chaoszhang/ASTER . Data The datasets scripts used in study https://github.com/ytabatabaee/CASTLES-Pro-paper

Language: Английский

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Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae)

PhytoKeys, Journal Year: 2022, Volume and Issue: 205, P. 3 - 58

Published: Aug. 22, 2022

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically economically important group trees, shrubs lianas a pantropical distribution. Despite major advances last few decades towards aligning clades across Caesalpinioideae, generic delimitation remains state considerable flux, especially mimosoid clade. We test monophyly via phylogenomic analysis 997 nuclear genes sequenced targeted enrichment (Hybseq) for 420 147 currently recognised subfamily. show that 22 are non-monophyletic or nested other non-monophyly concentrated clade where 25% 90 found to be non-monophyletic. suggest two main reasons this pervasive non-monophyly: (i) extensive morphological homoplasy we document here handful traits and, particularly, repeated evolution distinctive fruit types were historically emphasised delimiting (ii) artefact lack taxonomic syntheses sampling previous phylogenies consequent failure identify span Old World New conversely amphi-Atlantic non-monophyletic, both which critical large Finally, discuss taxon era how assessing patterns gene tree conflict can provide additional insights into delimitation. This new framework provides foundations series papers reclassifying presented

Language: Английский

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Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: June 6, 2022

Abstract Informed management and conservation efforts are vital to sustainable recreational fishing biodiversity conservation. Because the taxonomic rank of species is important in strategies, success these depends on accurate delimitation. The Black Basses ( Micropterus ) an iconic lineage freshwater fishes that include some world’s most popular for world's invasive species. Despite their popularity, previous studies delimit lineages suffer from insufficient geographic coverage uninformative molecular markers. Our phylogenomic analyses ddRAD data result delimitation 19 , which includes 14 described species, undescribed but well-known Altamaha, Bartram’s, Choctaw basses, two additional currently classified as Smallmouth Bass M. dolomieu ). We provide a revised Largemouth complex necessitates change scientific nomenclature: salmoides retained Florida nigricans elevated synonymy Bass. new understanding diversity, distribution, systematics will serve basis this charismatic economically clade fishes.

Language: Английский

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UCE phylogenomics, biogeography, and classification of long-horned bees (Hymenoptera: Apidae: Eucerini), with insights on using specimens with extremely degraded DNA

Insect Systematics and Diversity, Journal Year: 2023, Volume and Issue: 7(4)

Published: July 1, 2023

Abstract Long-horned bees (Apidae, Eucerini) are found in different biomes worldwide and include some important crop pollinators. In the Western Hemisphere, Eucerini received extensive taxonomic study during twentieth century, resulting several revisions of its genera. contrast, progress on eucerine phylogenetic research genus-level classification has been slow, primarily due to relatively homogeneous external morphology within tribe rarity many species collections. Here, we present a comprehensive based ultraconserved elements, including 153 from nearly all genera subgenera biogeographic regions where they occur. Many these specimens museums were collected as far back 1909. We discuss challenges working with highly degraded DNA, insights into improving results for both species-tree concatenation approaches, new pipeline UCE curation (Curation UltraconseRved Elements—CURE). Our show existence seven main lineages most be reciprocally monophyletic. Using up-to-date framework, we: (1) propose changes, subtribal reorganized generic subgeneric limits; (2) estimate divergence times; (3) conduct detailed exploration historical biogeography long-horned bees. find that expanded their range onto continents only after initial diversification southern South America Eocene.

Language: Английский

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Disentangling a genome-wide mosaic of conflicting phylogenetic signals in Western Rattlesnakes

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 108309 - 108309

Published: Feb. 1, 2025

Language: Английский

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An investigation of irreproducibility in maximum likelihood phylogenetic inference

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Nov. 30, 2020

Abstract Phylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515 (18.11%) IQ-TREE-inferred and 1813 (9.34%) RAxML-NG-inferred maximum likelihood (ML) gene topologically irreproducible when executing two replicates (Run1 Run2) each of 19,414 alignments in 15 animal, plant, fungal phylogenomic datasets. Notably, coalescent-based ASTRAL species phylogenies inferred from Run1 Run2 sets individual 9/15 datasets, whereas concatenation-based twice the same supermatrix reproducible. Our simulations further show more likely to be incorrect than reproducible phylogenies. These results suggest a considerable fraction single-gene ML may irreproducible. Increasing inference will benefit providing analyses’ log files, which contain typically reported parameters (e.g., program, substitution model, number tree searches) also unreported ones random starting seed number, threads, processor type).

Language: Английский

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